Background

The first cases of COVID-19, an infection caused by SARS-CoV-2, was first discovered in 2019, and quickly spread across the globe. Since the beginning of the pandemic, COVID-19 has stressed healthcare systems, leading to the implementation of various public health measures and vaccination programs. In 2021, researchers and clinicians began to discover increased rates of infection and mortality being caused by specific strains of COVID-19. These variants, named variants of concern (VOCs), include Alpha, Beta, Gamma, Delta and Omicron.

This report will use publicly available data downloaded from the government of Canada website to better understand key trends of COVID-19 during 2021. In doing so, this report will create informative tables and figures for infections, mortality, and vaccination by province.



Methods

Data

The data used in this analysis is publicly available and can be found at the Canadian Government webiste. This report uses data from 2021, which was a key point in the pandemic with the introduction of variants of concern (VOC) and the COVID-19 vaccines. The report takes the data stratified by province. The variables of interest were infections, mortality and vaccination.

Table 1. Population sizes by province
Province Population Percent of total
Ontario 13,448,494 38.3
Quebec 8,164,361 23.2
British Columbia 4,648,055 13.2
Alberta 4,067,175 11.6
Manitoba 1,278,365 3.6
Saskatchewan 1,098,352 3.1
Nova Scotia 923,598 2.6
New Brunswick 747,101 2.1
Newfoundland and Labrador 519,716 1.5
Prince Edward Island 142,907 0.4
Northwest Territories 41,786 0.1
Nunavut 35,944 0.1
Yukon 35,874 0.1
Total 35,151,728 100.0

Notes: Data taken from population sizes from 2016 Data taken from the MapCan package.

Analysis

This report was conducted using r and rmarkdown using packages from the tidyverse for data cleaning and wrangling, ggplot2 for creating figures and mapcan for creating the chloropleth map. Descriptive characteristics of each metric, stratified by province.

This analysis will conduct three primary sub-analyses: i) infections by province over time; ii) mortality rate over the year, plotted over a map of Canada; and iii) percentage of vaccinated (partially and fully).



Results

Infections by VOC

Over the course of 2021, Canadian provinces were impacted by several waves. Many of them being caused by the introduction of new VOCs. As seen in Figure 1, Ontario and Québec (the two most populous province), had the largest spikes in cases per day, totaling from 5,000 to 8,000. These large spikes overlapped with certain VOCs, for instance Ontario had its largest spike in cases during the Alpha and Gamma waves, while Québec had theirs during the Omicron wave.

Figure 1. Infections and variants in 2021

Figure 1. Infections and variants in 2021

Mortality rates

When looking at mortality rates by 100,000 people, Québec had the highest rates, with about 2.5 deaths per 100,000 (Figure 2). This was followed by Manitoba, which had a rate of approximately 2/100,000. Nunavut had the smallest rate, with less than 1 death per 100,000 people.

Figure 2. Map of mortality rates

Figure 2. Map of mortality rates

Vaccination

The vaccination program in Canada began in early 2021. The vaccination strategy differed from province to province, with some provinces giving second vaccinations 2 weeks after the first, while other province aimed to get the majority of the province partially vaccinated before the second dose. A wide range of vaccinations were used in Canada, mRNA and non-mRNA vaccines.

As can be seen by figure 3, within the first 6 months of the vaccination program, about 45% of individuals were vaccinated.It was around June 2021, where the majority of individuals started receiving their second doses. At the end of the calendar year, over 80% of eligible Canadians had been fully vaccinated.

Figure 4. Proportion of vaccinated

Figure 4. Proportion of vaccinated



Conclusions

This brief analysis summarised important characteristics of the COVID-19 pandemic in Canada in 2021. The aim of this analysis was to demonstrate how an analysis pipeline can be incorporated into the a workflow which produces an automated report, which allows ease of communication of findings with colleagues and other stakeholders.